Contacts of the strand formed by residues 153 - 161 (chain D) in PDB entry 4OA5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D VAL* 5.1 0.4 - - + -
129D PRO* 4.5 0.7 - - - -
130D PHE* 3.4 24.5 - - + +
131D ASP 4.0 4.9 - - - +
132D MET 3.7 26.5 - - - +
133D ILE* 3.8 13.5 - - + +
148D TRP* 4.3 9.0 - - + -
149D ALA* 2.9 36.7 + - + +
151D MET 4.5 2.5 - - - +
152D TYR* 1.3 79.5 + - - +
154D ARG* 1.3 71.9 + - - +
157D GLY* 3.9 21.8 - - - -
158D LEU 4.1 5.4 - - - +
159D ILE* 5.0 1.3 - - + -
216D LYS* 2.8 35.7 + - + -
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA* 4.5 14.3 + - - +
56D GLY 5.2 3.2 + - - -
57D ILE* 4.6 6.1 - - - +
129D PRO* 4.0 14.7 - - + +
130D PHE 3.0 19.3 + - - +
131D ASP* 2.8 33.9 + - - +
153D ILE* 1.3 78.0 - - - +
155D LYS* 1.3 81.3 + - - +
156D GLY* 3.4 23.2 + - - -
157D GLY* 2.9 28.3 + - - +
216D LYS* 3.7 5.4 - - - +
321D IOD 3.7 20.4 - - + -
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Residues in contact with LYS 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ILE 3.7 0.6 + - - -
154D ARG* 1.3 96.2 + - - +
156D GLY* 1.3 60.6 + - - +
216D LYS* 3.9 2.6 - - - +
217D LEU 3.6 20.4 + - - +
218D THR* 3.4 35.3 + - - +
313D IOD 4.2 14.8 - - + -
321D IOD 3.7 15.9 - - + +
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Residues in contact with GLY 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA* 6.0 1.7 - - - +
57D ILE* 5.9 0.5 - - - +
154D ARG* 3.4 16.7 + - - -
155D LYS* 1.3 72.3 - - - +
157D GLY* 1.3 62.2 + - - +
158D LEU* 4.9 4.5 - - - +
215D ILE* 3.8 12.8 - - - +
216D LYS 2.7 21.3 + - - -
313D IOD 3.9 18.2 - - - -
314D IOD 4.7 2.0 - - - -
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Residues in contact with GLY 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ILE* 5.6 0.4 - - - -
131D ASP 3.2 15.3 - - - -
153D ILE* 3.9 8.5 - - - -
154D ARG* 2.9 26.8 + - - -
155D LYS 3.1 1.6 + - - -
156D GLY* 1.3 81.0 - - - +
158D LEU* 1.3 61.2 + - - -
215D ILE* 3.5 2.8 - - - -
216D LYS* 2.9 27.4 + - - +
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 4.2 20.0 - - + +
55D ALA* 3.9 25.6 - - + -
57D ILE* 4.1 20.6 - - + -
131D ASP 2.9 7.1 + - - -
132D MET* 3.2 22.4 - - + -
133D ILE* 3.0 26.6 + - - +
153D ILE* 4.1 2.3 - - - +
156D GLY 4.9 3.1 - - - +
157D GLY* 1.3 75.0 - - - +
159D ILE* 1.3 62.4 + - - +
160D VAL* 4.0 10.5 - - + -
213D VAL* 5.0 10.8 - - + -
214D SER 3.3 13.0 - - - +
215D ILE* 3.8 22.4 - - + -
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Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 3.8 21.5 - - + -
135D ILE* 4.4 14.1 - - + -
146D LEU* 3.9 30.3 - - + -
149D ALA* 4.2 13.0 - - + -
150D LYS* 5.3 0.7 - - + +
153D ILE* 5.0 3.6 - - + -
158D LEU* 1.3 77.0 - - - +
160D VAL* 1.3 61.6 + - - +
190D PHE* 4.6 4.9 - - + -
194D LEU* 4.2 15.7 - - + -
200D TYR* 4.1 21.3 - - + -
212D MET* 3.8 2.6 - - + +
213D VAL* 3.6 1.6 + - - -
214D SER* 2.8 45.7 + - - +
216D LYS* 4.3 21.3 - - + -
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 3.9 19.3 - - + -
51D LEU* 4.4 13.5 - - + -
132D MET* 3.9 21.3 - - + -
133D ILE 2.9 11.7 + - - +
134D PHE* 3.3 20.1 - - + -
135D ILE* 2.8 33.4 + - - +
158D LEU* 4.3 14.8 - - + -
159D ILE* 1.3 79.7 - - - +
161D ALA* 1.3 58.6 + - - +
211D MET* 3.9 12.1 - - + -
212D MET* 3.2 12.8 - - - +
213D VAL* 4.4 10.1 - - + -
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 4.5 1.1 - - - -
135D ILE* 3.2 18.6 - - + +
142D TYR* 3.8 13.5 - - + -
160D VAL* 1.3 78.9 - - - +
162D ASP* 1.3 61.6 + - - +
164D THR* 3.6 7.0 - - + +
190D PHE* 3.7 30.1 - - + -
211D MET* 3.5 6.3 - - - -
212D MET* 2.8 37.9 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il